From: ftp-bimas.cit.nih.gov                      Last mod: June 27, 1999

               A new method of selecting loop breakers
                  Alejandro A. Schaffer

|*| Selecting loop breakers easily and automatically

  Exercise 7 on pages 93--96 of Handbook of Human Genetic Linkage
by Ott and Terwilliger describes a complicated, interactive method
to break loops using the makeped program and the LOOPS program
LOOPS [Xie X, Ott J: Finding all loops in a pedigree. 
Am J Hum Genet 1992; 51:A205].
As a result of innovations in FASTLINK 4.0P and FASTLINK 4.1P,
their method is now obsolete.

The new method is as follows:

1. When running your pre-makeped file through makeped, ALWAYS say
that the pedigrees have no loops, even if they do.
2. Put the post-makeped pedigree file in pedfile.dat.
3. Put the locus file in datafile.dat.
4. Run
     unknown -l

Note that the flag is the letter 'l', not the number '1'.
This will produce a new output file called
     lpedfile.dat
which has all the loops broken for you.

If your goal is to run an lcp-produced script
with pedigree file in pedin.dat and locus file in
datain.dat, you then

5. Copy lpedile.dat to pedin.dat
6  Copy the locus file to datain.dat

and run your script.

You will see diagnostic output showing that unknown is still trying
to find a better loop breaker set for you during the running of
the lcp-produced script. The reasons are as follows.

A. Your pedigree file may have dozens of loci while any specific
analysis may have only 2 or 3. The initial loop breaker set
selected by 
    unknown -l
attempts to be good for all loci, but may not be optimal for
any specific locus subset.

B. The method used during the main run uses a more precise
weight function to choose among the loop breaker possibilities
than does the preliminary run of
   unknown -l